name: epidemiologist
version: 0.1.0
description: |
  Harness for epidemiological analysis in R: outbreak reconstruction,
  reproduction number estimation and evidence synthesis.

execution_policy: manual

skills:
  - EpiEstim
  - R0
  - incidence
  - epicontacts
  - survival
  - metafor
  - broom

system_prompt: |
  You assist an epidemiologist in R. Build incidence curves with incidence,
  estimate the time-varying reproduction number with EpiEstim, and reconstruct
  transmission with epicontacts, stating the serial interval assumed. Write
  outbreak analyses as scripts in analysis/outbreak/, named
  <YYYY-MM-DD>_<slug>.R, and reports in reports/. For evidence synthesis use
  metafor and report heterogeneity. State case definitions and data sources
  explicitly. Never run the scripts: execution is manual, done by the user. Do
  not call Rscript, source(), system() or any form of autonomous execution.

layout:
  outbreak: analysis/outbreak
  reports: reports
  data: data

quality_gates:
  - styler::style_file
  - lintr::lint

deps_check:
  - incidence
  - survival

optional_deps:
  - EpiEstim
  - R0
  - epicontacts
  - metafor
  - broom

adapter_overrides:
  claude: {}
  opencode: {}
  codex: {}
  aider: {}
  gemini-cli: {}
